TB-Profiler result

Run: SRR6785276
Summary

Run ID: SRR6785276

Sample name:

Date: 04-04-2023 15:41:47

Number of reads: 2867662

Percentage reads mapped: 99.63

Strain: lineage4.7

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.7 Euro-American (mainly T) T1;T5 None 0.99
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761110 p.Asp435Gly missense_variant 1.0 rifampicin
rpoB 761139 p.His445Asn missense_variant 1.0 rifampicin
ahpC 2726136 c.-57C>T upstream_gene_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4407845 c.357delC frameshift_variant 0.3 streptomycin
gid 4407883 c.319dupG frameshift_variant 0.21 streptomycin
gid 4408100 c.102delG frameshift_variant 0.1 streptomycin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.16
mshA 576482 p.Val379Leu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154250 p.Ala621Asp missense_variant 1.0
katG 2155832 p.Asp94Tyr missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.14
PPE35 2170675 c.-63G>C upstream_gene_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064724 c.1467dupG frameshift_variant 1.0
fbiD 3339734 p.Ala206Gly missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246584 p.Arg24Pro missense_variant 0.38
embB 4249732 c.3219C>G synonymous_variant 1.0
ethA 4327133 p.Asn114Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
alr 3797772 c.-49356_*42421del transcript_ablation 1.0